Package: orderly2 1.99.59

Rich FitzJohn

orderly2: Orderly Next Generation

Distributed reproducible computing framework, adopting ideas from git, docker and other software. By defining a lightweight interface around the inputs and outputs of an analysis, a lot of the repetitive work for reproducible research can be automated. We define a simple format for organising and describing work that facilitates collaborative reproducible research and acknowledges that all analyses are run multiple times over their lifespans.

Authors:Rich FitzJohn [aut, cre], Robert Ashton [aut], Martin Eden [aut], Alex Hill [aut], Wes Hinsley [aut], Mantra Kusumgar [aut], Paul Liétar [aut], James Thompson [aut], Imperial College of Science, Technology and Medicine [cph]

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orderly2.pdf |orderly2.html✨
orderly2/json (API)

# Install 'orderly2' in R:
install.packages('orderly2', repos = c('https://mrc-ide.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/mrc-ide/orderly2/issues

On CRAN:

8.33 score 8 stars 2 packages 49 scripts 50 exports 23 dependencies

Last updated 3 hours agofrom:d9ab97c954 (on main). Checks:OK: 6 ERROR: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 13 2024
R-4.5-winOKDec 13 2024
R-4.5-linuxERRORDec 13 2024
R-4.4-winOKDec 13 2024
R-4.4-macOKDec 13 2024
R-4.3-winOKDec 13 2024
R-4.3-macOKDec 13 2024

Exports:orderly_artefactorderly_cleanuporderly_cleanup_statusorderly_compare_packetsorderly_comparison_explainorderly_configorderly_config_setorderly_copy_filesorderly_dependencyorderly_descriptionorderly_exampleorderly_gitignore_updateorderly_hash_dataorderly_hash_fileorderly_initorderly_interactive_set_search_optionsorderly_list_srcorderly_location_addorderly_location_add_httporderly_location_add_packitorderly_location_add_pathorderly_location_fetch_metadataorderly_location_listorderly_location_pullorderly_location_pull_metadataorderly_location_pull_packetorderly_location_pushorderly_location_removeorderly_location_renameorderly_metadataorderly_metadata_extractorderly_metadata_readorderly_neworderly_parametersorderly_parse_exprorderly_parse_fileorderly_plugin_add_metadataorderly_plugin_contextorderly_plugin_registerorderly_prune_orphansorderly_queryorderly_query_explainorderly_resourceorderly_runorderly_run_infoorderly_searchorderly_search_optionsorderly_shared_resourceorderly_strict_modeorderly_validate_archive

Dependencies:askpassclicrayoncredentialscurldiffobjfsgertgluehttr2jsonlitelifecyclemagrittropensslR6rappdirsrlangrstudioapisysvctrswithryamlzip

Collaborative analysis

Rendered fromcollaboration.Rmdusingknitr::rmarkdownon Dec 13 2024.

Last update: 2024-10-24
Started: 2023-08-07

Creating plugins

Rendered fromplugins.Rmdusingknitr::rmarkdownon Dec 13 2024.

Last update: 2024-02-29
Started: 2023-07-26

Dependencies between packets

Rendered fromdependencies.Rmdusingknitr::rmarkdownon Dec 13 2024.

Last update: 2024-10-24
Started: 2023-08-07

Introduction to orderly2

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Dec 13 2024.

Last update: 2024-10-22
Started: 2023-07-20

Migrating from orderly (1.x)

Rendered frommigrating.Rmdusingknitr::rmarkdownon Dec 13 2024.

Last update: 2024-02-29
Started: 2023-07-20

Orderly query DSL

Rendered fromquery.Rmdusingknitr::rmarkdownon Dec 13 2024.

Last update: 2023-11-20
Started: 2023-07-20

orderly2

Rendered fromorderly2.Rmdusingknitr::rmarkdownon Dec 13 2024.

Last update: 2024-11-19
Started: 2023-07-20

Outpack metadata

Rendered frommetadata.Rmdusingknitr::rmarkdownon Dec 13 2024.

Last update: 2024-08-14
Started: 2023-07-20

Troubleshooting

Rendered fromtroubleshooting.Rmdusingknitr::rmarkdownon Dec 13 2024.

Last update: 2024-10-22
Started: 2023-09-05

Readme and manuals

Help Manual

Help pageTopics
Declare orderly artefactsorderly_artefact
Clean up source directoryorderly_cleanup orderly_cleanup_status
Compare the metadata and contents of two packets.orderly_compare_packets
Print the details of a packet comparison.orderly_comparison_explain
Read configurationorderly_config
Set configuration optionsorderly_config_set
Copy files from a packetorderly_copy_files
Declare a dependencyorderly_dependency
Describe the current packetorderly_description
Copy a simple orderly exampleorderly_example
Update a gitignore fileorderly_gitignore_update
Compute a hashorderly_hash_data orderly_hash_file
Initialise an orderly repositoryorderly_init
Set search options for interactive useorderly_interactive_set_search_options
List source reportsorderly_list_src
Add a new locationorderly_location_add orderly_location_add_http orderly_location_add_packit orderly_location_add_path
Fetch metadata from a locationorderly_location_fetch_metadata
List known pack locationsorderly_location_list
Pull one or more packets from a locationorderly_location_pull
Push tree to locationorderly_location_push
Remove a locationorderly_location_remove
Rename a locationorderly_location_rename
Read outpack metadataorderly_metadata
Extract metadata from orderly2 packetsorderly_metadata_extract
Read outpack metadata json fileorderly_metadata_read
Create a new reportorderly_new
Declare orderly parametersorderly_parameters
Parse the orderly entrypoint scriptorderly_parse_expr orderly_parse_file
Add metadata from pluginorderly_plugin_add_metadata
Fetch plugin contextorderly_plugin_context
Register an orderly pluginorderly_plugin_register
Prune orphan packet metadataorderly_prune_orphans
Construct outpack queryorderly_query
Explain a queryorderly_query_explain
Declare orderly resourcesorderly_resource
Run a reportorderly_run
Information about currently running reportorderly_run_info
Query outpack's databaseorderly_search
Packet search optionsorderly_search_options
Copy shared resources into a packet directoryorderly_shared_resource
Enable orderly strict modeorderly_strict_mode
Validate unpacked packets.orderly_validate_archive